Amber 16 has been installed on the OSC clusters; usage is via the module amber/16. For information on available executables and installation details see the software page for Amber or the output of the module help command, e.g.: module help amber/16. On August 15, 2016 Amber 16 will be made the default amber module.
Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.
Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, integrating ordinary functions, manipulating polynomials, and integrating ordinary differential and differential-algebraic equations. It is easily extensible and customizable via user-defined functions written in Octave's own language, or using dynamically loaded modules written in C++, C, Fortran, or other languages.
While we provide a number of Python modules, you may need a module we do not provide. If it is a commonly used module, or one that is particularly difficult to compile, you can contact OSC Help for assistance, but we have provided an example below showing how to build and install your own Python modules, and make them available inside of Python. Note, these instructions use "bash" shell syntax; this is our default shell, but if you are using something else (csh, tcsh, etc), some of the syntax may be different.
OSC provides Allinea Performance Reports and Allinea MAP to all OSC users.
- Allinea Performance Reports: very simple tool to generate one single-page HTML report that presents overall performance characteristics of HPC applications
- Allinea MAP: HPC application profiler with easy-to-use GUI environment.
The following versions of Allinea are available on OSC clusters:
Sometimes the best way to get access to a piece of software on the HPC systems is to install it yourself as a "local install". This document will walk you through the OSC-recommended procedure for maintaining local installs in your home directory or project space.
Comsol 5.2 has been installed on Ruby. To load, use
module load comsol/52
All ACLs set within the Home Directory filesystem (/nfs/##) were lost during the 6/7 downtime. This was caused by the migration to a new server that does not support the old POSIX ACLs.
Migrating the ACLs was not possible due to both the fact POSIX ACLs are not easily translatable to NFSv4 ACLs, and none of our tools supported such a migration.
OSCusage is command developed at OSC for use on OSC's systems. It allows for a user to see information on their project's current RU balance, including which users and jobs incurred what charges.
An eligible principal investigator (PI) heads a project account and can authorize/remove user accounts under the project account (please check our Allocations and Accounts documentation for more details). This document shows you how to identify users on a project account and check the status of each user.
We have been adding some output from
qsub that should aid you in creating better job scripts. We've documented the various messages here.
A "NOTE" message is informational; your job has been submitted, but
qsub made some assumptions about your job that you may not have intended.